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<h1>Isotopic peaks grouper</h1>

<h2>Description</h2>

<p>
This module attempts to find those peaks in a scan, which form an isotope pattern. 
When isotope pattern is found, the information about the charge and isotope ratios is saved, and additional isotopic peaks are removed from the peak list. 
Only the highest/lightest isotopic peak is kept. 
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<h4>Method parameters</h4>
<dl>

<dt>m/z tolerance</dt>
<dd>Maximum distance in m/z from the expected location of a peak</dd>

<dt>Monotonic shape</dt>
<dd>If true, then monotonically decreasing height of isotope pattern is required</dd>

<dt>Maximum charge</dt>
<dd>Maximum charge to consider for detecting the isotope patterns</dd>

<dt>Representative isotope</dt>
<dd>Which peak should represent the whole isotope pattern. For small molecular weight
          compounds with monotonically decreasing isotope pattern, the most intense isotope
          should be representative. For high molecular weight peptides, the lowest m/z
          peptides, the lowest m/z isotope may be the representative.</dd>

<dt>Remove non-isotopes</dt>
<dd>If checked, all peaks without an isotope pattern will not be displayed and not passed to the next module.</dd>

<dt>Display results</dt>
<dd>If enabled, the result will be displayed in the spectrum plot. If this is the last module in the processing list, the results will be displayed in any way.</dd>
						
<dt>Dataset color</dt>
<dd>Select the color, the results of this module shall be displayed in.</dd>

<h2>Deisotoping algorithm</h2>

<p>
Peaks in the peak list are processed in the order of decreasing height.
For each peak, MZmine tries to find the most appropriate charge state by comparing the number of identified isotopes for each possible charge. 
For each charge state, peaks which fit the m/z and RT distance limits are considered as isotopes.
The charge state with the highest number of identified isotopes is selected, and the isotope pattern is generated.
</p>

<h3>Mass difference between isotopes</h3>

<p>
The difference between neighboring isotopes is a single neutron.
The exact mass of 1 neutron is 1.008665 Da, but part of this mass is
consumed as a binding energy to other nucleons.
This small difference may become significant with high-resolution MS data.
The actual mass difference between isotopes depends on the chemical formula of the molecule. 
Since MZmine does not know the formula at the time of deisotoping, it assumes the default distance
of ~1.0033 Da, with user-defined tolerance (the m/z tolerance parameter).
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